--- Rachel Alcraft, Bioinformatics ---

Bioinformatics Code

These projects have been developed as a result of studying at Birkbeck College, UK

PsuGeometry

This is a python library to produce geoemntric analyses of protein structures, including the secondary structure information from dssp and the electron density information from ccp4 files where available. The images produced range from a simple Ramachandran plot than can be coloured on for example secondary structure, electron density or B-Factor, to say, a correlation of number of electrons against B-Factor. The library contains some pre-created reports so the code to create seom fairly involved reports is minimal.

PsuGeomtery help and documentaiton is here

Density Flight

Density Flight is a windows application to view the inside of an electron density matrix. The application allows you to navigate around like a flight simulator, viewing atoms, bonds between atoms, finding density peaks, rotateing in the space to seek planar atoms.
The application can currently be downloaded from github and built in Vsiual Studio 2019 (C#)
It will be available for beta testing in the windows store shortly.

Density Flight help and documentaiton is here

PsuGeometry Example

These links show some examples of images and reports produced by PsuGeometry:

• Cryo EM examples:
• Data and density:
• Correlations:
• Matching ProCheck:

Density Peaks and Atoms Comparison

PSU: Geometric Correlations

Row 8
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Contact Rachel Alcraft by email, (Rachel's email)
Return to Rachel's home page - rachelalcraft.github.io
For notes on citations for this work click here